@genome-spy/core 0.70.0 → 0.72.0

package/dist/schema.json

@@ -997,10 +997,6 @@
           },
           "type": "array"
         },
-        "configurableVisibility": {
-          "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-          "type": "boolean"
-        },
         "data": {
           "$ref": "#/definitions/Data",
           "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -1571,10 +1567,6 @@
               "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
               "type": "string"
             },
-            "configurableVisibility": {
-              "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-              "type": "boolean"
-            },
             "data": {
               "$ref": "#/definitions/Data",
               "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -1927,10 +1919,6 @@
               "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
               "type": "string"
             },
-            "configurableVisibility": {
-              "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-              "type": "boolean"
-            },
             "data": {
               "$ref": "#/definitions/Data",
               "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -2290,10 +2278,6 @@
               "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
               "type": "string"
             },
-            "configurableVisibility": {
-              "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-              "type": "boolean"
-            },
             "data": {
               "$ref": "#/definitions/Data",
               "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -2658,10 +2642,6 @@
               "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
               "type": "string"
             },
-            "configurableVisibility": {
-              "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-              "type": "boolean"
-            },
             "data": {
               "$ref": "#/definitions/Data",
               "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -3023,10 +3003,6 @@
               "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
               "type": "string"
             },
-            "configurableVisibility": {
-              "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-              "type": "boolean"
-            },
             "data": {
               "$ref": "#/definitions/Data",
               "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -3405,10 +3381,6 @@
               },
               "type": "array"
             },
-            "configurableVisibility": {
-              "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-              "type": "boolean"
-            },
             "data": {
               "$ref": "#/definitions/Data",
               "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -5455,10 +5427,6 @@
           "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
           "type": "string"
         },
-        "configurableVisibility": {
-          "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-          "type": "boolean"
-        },
         "data": {
           "$ref": "#/definitions/Data",
           "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -6097,10 +6065,6 @@
           "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
           "type": "string"
         },
-        "configurableVisibility": {
-          "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-          "type": "boolean"
-        },
         "data": {
           "$ref": "#/definitions/Data",
           "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -6923,10 +6887,6 @@
           "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
           "type": "string"
         },
-        "configurableVisibility": {
-          "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-          "type": "boolean"
-        },
         "data": {
           "$ref": "#/definitions/Data",
           "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -10140,10 +10100,6 @@
           "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
           "type": "string"
         },
-        "configurableVisibility": {
-          "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-          "type": "boolean"
-        },
         "data": {
           "$ref": "#/definitions/Data",
           "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."
@@ -10568,10 +10524,6 @@
           "description": "The base URL for relative URL data sources and URL [imports](https://genomespy.app/docs/grammar/import/#importing-from-a-url). The base URLs are inherited in the view hierarchy unless overridden with this property. By default, the top-level view's base URL equals to the visualization specification's base URL.",
           "type": "string"
         },
-        "configurableVisibility": {
-          "description": "Is the visibility configurable interactively from the [GenomeSpy App](https://genomespy.app/docs/sample-collections/). Configurability requires that the view has an explicitly specified name that is unique within its import scope.\n\n**Default:** `false` for children of `layer`, `true` for others.",
-          "type": "boolean"
-        },
         "data": {
           "$ref": "#/definitions/Data",
           "description": "Specifies a [data source](https://genomespy.app/docs/grammar/data/). If omitted, the data source is inherited from the parent view."

package/dist/src/data/formats/parquet.d.ts

@@ -0,0 +1,12 @@
+/**
+ * Load a data set in Apache Parquet format for use in Vega.
+ * @param {ArrayBuffer|Uint8Array} data Parquet binary data.
+ * @returns {Promise<Record<string,any>[]>} A promise that resolves to an array of data objects representing
+ *  rows of a data table.
+ */
+declare function parquet(data: ArrayBuffer | Uint8Array): Promise<Record<string, any>[]>;
+declare namespace parquet {
+    let responseType: string;
+}
+export default parquet;
+//# sourceMappingURL=parquet.d.ts.map

package/dist/src/data/formats/parquet.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parquet.d.ts","sourceRoot":"","sources":["../../../../src/data/formats/parquet.js"],"names":[],"mappings":"AAYA;;;;;GAKG;AACH,+BAJW,WAAW,GAAC,UAAU,GACpB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAC,GAAG,CAAC,EAAE,CAAC,CAWzC"}

package/dist/src/data/formats/parquet.js

@@ -0,0 +1,29 @@
+/*
+ * Adapted from: https://github.com/vega/vega-loader-parquet/blob/main/src/index.js
+ */
+
+/**
+ * @returns {Promise<typeof import("./parquetRead.js").parquetReadObjects>}
+ */
+async function loadParquetReadObjects() {
+    const { parquetReadObjects } = await import("./parquetRead.js");
+    return parquetReadObjects;
+}
+
+/**
+ * Load a data set in Apache Parquet format for use in Vega.
+ * @param {ArrayBuffer|Uint8Array} data Parquet binary data.
+ * @returns {Promise<Record<string,any>[]>} A promise that resolves to an array of data objects representing
+ *  rows of a data table.
+ */
+export default async function parquet(data) {
+    const parquetReadObjects = await loadParquetReadObjects();
+    const buffer =
+        data instanceof Uint8Array
+            ? /** @type {ArrayBuffer} */ (data.buffer)
+            : data;
+
+    return await parquetReadObjects({ file: buffer });
+}
+
+parquet.responseType = "arrayBuffer";

package/dist/src/data/formats/parquetRead.d.ts

@@ -0,0 +1,18 @@
+/**
+ * @param {ObjectParquetReadOptions} options
+ * @returns {Promise<void>}
+ */
+export function parquetRead(options: ObjectParquetReadOptions): Promise<void>;
+/**
+ * @param {Omit<ObjectParquetReadOptions, "onComplete">} options
+ * @returns {Promise<Record<string, any>[]>}
+ */
+export function parquetReadObjects(options: Omit<ObjectParquetReadOptions, "onComplete">): Promise<Record<string, any>[]>;
+/**
+ * Object-row variant of Parquet read options used by this trimmed reader.
+ */
+export type ObjectParquetReadOptions = Omit<import("hyparquet").ParquetReadOptions, "rowFormat" | "filter" | "filterStrict" | "onComplete"> & {
+    onComplete?: (rows: Record<string, any>[]) => void;
+};
+export type RowGroupObjectBuilder = (groupData: Record<string, any>[], selectStart: number, selectCount: number, columnData: import("hyparquet").DecodedArray[], columnSkipped: number[]) => Record<string, any>[];
+//# sourceMappingURL=parquetRead.d.ts.map

package/dist/src/data/formats/parquetRead.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"parquetRead.d.ts","sourceRoot":"","sources":["../../../../src/data/formats/parquetRead.js"],"names":[],"mappings":"AAqOA;;;GAGG;AACH,qCAHW,wBAAwB,GACtB,OAAO,CAAC,IAAI,CAAC,CAiFzB;AAED;;;GAGG;AACH,4CAHW,IAAI,CAAC,wBAAwB,EAAE,YAAY,CAAC,GAC1C,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAAE,CAAC,CAS1C;;;;uCAlTY,IAAI,CAChB,OAAU,WAAW,EAAE,kBAAkB,EACzC,WAAc,GAAG,QAAQ,GAAG,cAAc,GAAG,YAAY,CACtD,GAAG;IACH,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAAE,KAAK,IAAI,CAAA;CAClD;oCAIS,CACT,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAAE,EAChC,WAAW,EAAE,MAAM,EACnB,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,OAAO,WAAW,EAAE,YAAY,EAAE,EAC9C,aAAa,EAAE,MAAM,EAAE,KACnB,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAAE"}

package/dist/src/data/formats/parquetRead.js

@@ -0,0 +1,326 @@
+/*
+ * Adapted from hyparquet internals:
+ * https://github.com/hyparam/hyparquet (notably src/read.js and src/rowgroup.js).
+ *
+ * GenomeSpy-specific changes in this copy:
+ * - object-row output only (array row format removed)
+ * - filtering support removed
+ * - hot row transpose path optimized with cached codegen for typical schemas
+ * - fallback to interpreted row builder for very wide schemas
+ */
+
+import { parquetMetadataAsync, parquetSchema } from "hyparquet/src/metadata.js";
+import { parquetPlan, prefetchAsyncBuffer } from "hyparquet/src/plan.js";
+import { assembleAsync, readRowGroup } from "hyparquet/src/rowgroup.js";
+import { concat } from "hyparquet/src/utils.js";
+
+/**
+ * Object-row variant of Parquet read options used by this trimmed reader.
+ *
+ * @typedef {Omit<
+ *  import("hyparquet").ParquetReadOptions,
+ *  "rowFormat" | "filter" | "filterStrict" | "onComplete"
+ * > & {
+ *  onComplete?: (rows: Record<string, any>[]) => void
+ * }} ObjectParquetReadOptions
+ */
+
+/**
+ * @typedef {(
+ *  groupData: Record<string, any>[],
+ *  selectStart: number,
+ *  selectCount: number,
+ *  columnData: import("hyparquet").DecodedArray[],
+ *  columnSkipped: number[]
+ * ) => Record<string, any>[]} RowGroupObjectBuilder
+ */
+
+/** @type {Map<string, RowGroupObjectBuilder>} */
+const rowGroupObjectBuilderCache = new Map();
+
+const MAX_CODEGEN_COLUMNS = 200;
+
+/**
+ * @param {ObjectParquetReadOptions} options
+ * @returns {import("hyparquet").AsyncRowGroup[]}
+ */
+function parquetReadAsync(options) {
+    if (!options.metadata) {
+        throw new Error("parquet requires metadata");
+    }
+
+    const plan = parquetPlan(options);
+    options.file = prefetchAsyncBuffer(options.file, plan);
+
+    return plan.groups.map((groupPlan) =>
+        readRowGroup(options, plan, groupPlan)
+    );
+}
+
+/**
+ * Flatten decoded data pages into a single decoded array.
+ * This local version avoids chunked slice/push overhead in hot paths.
+ *
+ * @param {import("hyparquet").DecodedArray[] | undefined} chunks
+ * @returns {import("hyparquet").DecodedArray}
+ */
+function flattenColumnChunks(chunks) {
+    if (!chunks) {
+        return [];
+    }
+
+    if (chunks.length === 1) {
+        return chunks[0];
+    }
+
+    let totalLength = 0;
+    for (const chunk of chunks) {
+        totalLength += chunk.length;
+    }
+
+    const output = Array(totalLength);
+    let offset = 0;
+    for (const chunk of chunks) {
+        for (let i = 0; i < chunk.length; i++) {
+            output[offset + i] = chunk[i];
+        }
+        offset += chunk.length;
+    }
+
+    return output;
+}
+
+/**
+ * @param {string[]} columnNames
+ * @returns {RowGroupObjectBuilder}
+ */
+function getRowGroupObjectBuilder(columnNames) {
+    // Compile one builder per column layout to keep object writes monomorphic.
+    const signature = columnNames.join("\u001f");
+    const cached = rowGroupObjectBuilderCache.get(signature);
+    if (cached) {
+        return cached;
+    }
+
+    const assignments = columnNames
+        .map(
+            (columnName, i) =>
+                JSON.stringify(columnName) +
+                ": columnData[" +
+                i +
+                "][row - columnSkipped[" +
+                i +
+                "]]"
+        )
+        .join(",\n");
+
+    const builder = /** @type {RowGroupObjectBuilder} */ (
+        new Function(
+            "groupData",
+            "selectStart",
+            "selectCount",
+            "columnData",
+            "columnSkipped",
+            // Keep generated code focused on the tight row loop only.
+            "for (let selectRow = 0; selectRow < selectCount; selectRow++) {\n" +
+                "    const row = selectStart + selectRow;\n" +
+                "    groupData[selectRow] = {\n" +
+                assignments +
+                "\n" +
+                "    };\n" +
+                "}\n" +
+                "return groupData;"
+        )
+    );
+
+    rowGroupObjectBuilderCache.set(signature, builder);
+
+    return builder;
+}
+
+/**
+ * @param {Record<string, any>[]} groupData
+ * @param {number} selectStart
+ * @param {number} selectCount
+ * @param {string[]} columnNames
+ * @param {import("hyparquet").DecodedArray[]} columnData
+ * @param {number[]} columnSkipped
+ * @returns {Record<string, any>[]}
+ */
+function buildRowsInterpreted(
+    groupData,
+    selectStart,
+    selectCount,
+    columnNames,
+    columnData,
+    columnSkipped
+) {
+    for (let selectRow = 0; selectRow < selectCount; selectRow++) {
+        const row = selectStart + selectRow;
+        /** @type {Record<string, any>} */
+        const rowData = {};
+        for (let i = 0; i < columnNames.length; i++) {
+            rowData[columnNames[i]] = columnData[i][row - columnSkipped[i]];
+        }
+        groupData[selectRow] = rowData;
+    }
+
+    return groupData;
+}
+
+/**
+ * Object-only copy of hyparquet's asyncGroupToRows.
+ *
+ * @param {import("hyparquet").AsyncRowGroup} asyncGroup
+ * @param {number} selectStart
+ * @param {number} selectEnd
+ * @returns {Promise<Record<string, any>[]>}
+ */
+async function asyncGroupToRowsObject(
+    { asyncColumns },
+    selectStart,
+    selectEnd
+) {
+    // Resolve all async column pages once before entering the hot transpose loop.
+    const pages = await Promise.all(asyncColumns.map((column) => column.data));
+    const columnCount = asyncColumns.length;
+
+    /** @type {string[]} */
+    const columnNames = Array(columnCount);
+    /** @type {import("hyparquet").DecodedArray[]} */
+    const columnData = Array(columnCount);
+    /** @type {number[]} */
+    const columnSkipped = Array(columnCount);
+
+    // Precompute all indirections outside the generated function.
+    for (let i = 0; i < columnCount; i++) {
+        columnNames[i] = asyncColumns[i].pathInSchema[0];
+        columnData[i] = flattenColumnChunks(pages[i].data);
+        columnSkipped[i] = pages[i].skipped;
+    }
+
+    const selectCount = selectEnd - selectStart;
+
+    /** @type {Record<string, any>[]} */
+    const groupData = Array(selectCount);
+
+    // Avoid excessively large generated functions for very wide schemas.
+    if (columnCount > MAX_CODEGEN_COLUMNS) {
+        return buildRowsInterpreted(
+            groupData,
+            selectStart,
+            selectCount,
+            columnNames,
+            columnData,
+            columnSkipped
+        );
+    }
+
+    const buildRows = getRowGroupObjectBuilder(columnNames);
+
+    return buildRows(
+        groupData,
+        selectStart,
+        selectCount,
+        columnData,
+        columnSkipped
+    );
+}
+
+/**
+ * @param {ObjectParquetReadOptions} options
+ * @returns {Promise<void>}
+ */
+export async function parquetRead(options) {
+    if ("rowFormat" in options) {
+        throw new Error(
+            'parquetRead supports only object rows; use rowFormat: "object" implicitly'
+        );
+    }
+    if ("filter" in options || "filterStrict" in options) {
+        throw new Error("parquetRead does not support filtering");
+    }
+
+    options.metadata ??= await parquetMetadataAsync(options.file, options);
+
+    const { rowStart = 0, rowEnd, onChunk, onComplete } = options;
+
+    const asyncGroups = parquetReadAsync(options);
+
+    if (!onComplete && !onChunk) {
+        for (const { asyncColumns } of asyncGroups) {
+            for (const { data } of asyncColumns) {
+                await data;
+            }
+        }
+        return;
+    }
+
+    const schemaTree = parquetSchema(options.metadata);
+    const assembled = asyncGroups.map((group) =>
+        assembleAsync(group, schemaTree, options.parsers)
+    );
+
+    if (onChunk) {
+        for (const asyncGroup of assembled) {
+            for (const asyncColumn of asyncGroup.asyncColumns) {
+                asyncColumn.data.then(
+                    /**
+                     * @param {{ data: import("hyparquet").DecodedArray[]; skipped: number }} chunk
+                     */
+                    (chunk) => {
+                        let chunkRowStart =
+                            asyncGroup.groupStart + chunk.skipped;
+                        for (const columnData of chunk.data) {
+                            onChunk({
+                                columnName: asyncColumn.pathInSchema[0],
+                                columnData,
+                                rowStart: chunkRowStart,
+                                rowEnd: chunkRowStart + columnData.length,
+                            });
+                            chunkRowStart += columnData.length;
+                        }
+                    }
+                );
+            }
+        }
+    }
+
+    if (onComplete) {
+        /** @type {Record<string, any>[]} */
+        const rows = [];
+        for (const asyncGroup of assembled) {
+            const selectStart = Math.max(rowStart - asyncGroup.groupStart, 0);
+            const selectEnd = Math.min(
+                (rowEnd ?? Infinity) - asyncGroup.groupStart,
+                asyncGroup.groupRows
+            );
+            const groupData = await asyncGroupToRowsObject(
+                asyncGroup,
+                selectStart,
+                selectEnd
+            );
+            concat(rows, groupData);
+        }
+        onComplete(rows);
+    } else {
+        for (const { asyncColumns } of assembled) {
+            for (const { data } of asyncColumns) {
+                await data;
+            }
+        }
+    }
+}
+
+/**
+ * @param {Omit<ObjectParquetReadOptions, "onComplete">} options
+ * @returns {Promise<Record<string, any>[]>}
+ */
+export function parquetReadObjects(options) {
+    return new Promise((onComplete, reject) => {
+        parquetRead({
+            ...options,
+            onComplete,
+        }).catch(reject);
+    });
+}

package/dist/src/data/sources/urlSource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AASA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CAuGxC;uBAtIsB,iBAAiB"}
+{"version":3,"file":"urlSource.d.ts","sourceRoot":"","sources":["../../../../src/data/sources/urlSource.js"],"names":[],"mappings":"AASA;;;GAGG;AACH,gCAHW,OAAO,CAAC,OAAO,oBAAoB,EAAE,IAAI,CAAC,GACxC,IAAI,IAAI,OAAO,oBAAoB,EAAE,OAAO,CAIxD;AAED;IACI;;;OAGG;IACH,oBAHW,OAAO,oBAAoB,EAAE,OAAO,QACpC,OAAO,oBAAoB,EAAE,OAAO,EAc9C;IATG,6CAMC;IAED,gBAAiC;;CA4GxC;uBA3IsB,iBAAiB"}

package/dist/src/data/sources/urlSource.js

@@ -110,15 +110,20 @@ export default class UrlSource extends DataSource {
          * @param {any} content
          * @param {string} [url]
          */
-        const readAndParse = (content, url) => {
+        const readAndParse = async (content, url) => {
             try {
-                /** @type {any[]} */
-                const data = read(content, format);
+                /** @type {any[] | Promise<any[]>} */
+                const dataOrPromise = read(content, format);
+                const data =
+                    dataOrPromise instanceof Promise
+                        ? await dataOrPromise
+                        : dataOrPromise;
                 this.beginBatch({ type: "file", url: url });
                 for (const d of data) {
                     this._propagate(d);
                 }
             } catch (e) {
+                console.warn(e);
                 throw new Error(`Cannot parse: ${url}: ${e.message}`);
             }
         };

package/dist/src/encoder/encoder.d.ts

@@ -54,12 +54,12 @@ export function isChannelDefWithScale(channelDef: import("../spec/channel.js").C
 /**
  * @param {import("../spec/channel.js").ChannelDef} channelDef
  */
-export function findChannelDefWithScale(channelDef: import("../spec/channel.js").ChannelDef): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<string | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<number | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins);
+export function findChannelDefWithScale(channelDef: import("../spec/channel.js").ChannelDef): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<string | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").ValueDefBase<number | import("../spec/parameter.js").ExprRef> & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>) | (import("../spec/channel.js").ParameterPredicate & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").DomainContributionMixins);
 /**
  * @param {import("../view/unitView.js").default} view
  * @param {import("../spec/channel.js").Channel} channel
  */
-export function getChannelDefWithScale(view: import("../view/unitView.js").default, channel: import("../spec/channel.js").Channel): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").PositionDatumDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").TypeForShape>, string> | (import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ChromPosDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<"locus"> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").XIndexDef);
+export function getChannelDefWithScale(view: import("../view/unitView.js").default, channel: import("../spec/channel.js").Channel): import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, string> | import("../spec/channel.js").PositionFieldDef | import("../spec/channel.js").ChromPosDef | import("../spec/channel.js").PositionDatumDef | (import("../spec/channel.js").FieldDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ChromPosDefBase & import("../spec/channel.js").TitleMixins & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<"locus"> & import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").XIndexDef) | (import("../spec/channel.js").ScaleMixins & import("../spec/channel.js").DatumDef<import("../spec/parameter.js").ExprRef | import("../spec/channel.js").Scalar> & import("../spec/channel.js").DomainContributionMixins & import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type> & import("../spec/channel.js").PositionMixins & import("../spec/channel.js").XIndexDef) | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").Type>, number> | import("../spec/channel.js").FieldOrDatumDefWithCondition<import("../spec/channel.js").MarkPropFieldDef<import("../spec/channel.js").TypeForShape>, string>;
 /**
  * @param {import("../spec/channel.js").ChannelDef} channelDef
  * @returns {channelDef is import("../spec/channel.js").TypeMixins<import("../spec/channel.js").Type>}

package/dist/src/fonts/bmFontManager.d.ts

@@ -51,7 +51,7 @@ export default class BmFontManager {
      * @param {FontWeight | keyof WEIGHTS} weight
      * @returns {FontEntry}
      */
-    getFont(family: string, style?: FontStyle, weight?: FontWeight | ("bold" | "normal" | "medium" | "thin" | "light" | "regular" | "black")): FontEntry;
+    getFont(family: string, style?: FontStyle, weight?: FontWeight | ("bold" | "normal" | "thin" | "light" | "regular" | "medium" | "black")): FontEntry;
     /**
      *
      * @param {FontEntry} fontEntry An uninitialized font entry

package/dist/src/genome/genome.d.ts

@@ -60,9 +60,9 @@ export default class Genome {
      */
     constructor(config: GenomeConfig);
     config: {
+        url: string;
         name: string;
     } | {
-        url: string;
         name: string;
     } | {
         contigs: import("../spec/genome.js").Contig[];

package/dist/src/genomeSpy/containerUi.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"containerUi.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/containerUi.js"],"names":[],"mappings":"AAGA;;GAEG;AACH,6CAFW,WAAW;;;;;EA6BrB;AAED;;;GAGG;AACH,4CAHW,WAAW,WACX,MAAM,QAUhB;oBA9CmB,wBAAwB"}
+{"version":3,"file":"containerUi.d.ts","sourceRoot":"","sources":["../../../src/genomeSpy/containerUi.js"],"names":[],"mappings":"AAGA;;GAEG;AACH,6CAFW,WAAW;;;;;EA4BrB;AAED;;;GAGG;AACH,4CAHW,WAAW,WACX,MAAM,QAUhB;oBA7CmB,wBAAwB"}

package/dist/src/genomeSpy/containerUi.js

@@ -21,7 +21,6 @@ export function createContainerUi(container) {
     const loadingIndicatorsElement = element("div", {
         class: "loading-indicators",
     });
-    canvasWrapper.appendChild(loadingIndicatorsElement);
 
     const tooltip = new Tooltip(container);
 

package/dist/src/genomeSpy/viewHighlight.js

@@ -8,7 +8,7 @@ export function createViewHighlighter(container) {
     return (view) => {
         container.querySelector(".view-highlight")?.remove();
         if (view) {
-            if (!view.isConfiguredVisible()) {
+            if (!view.isVisible()) {
                 return;
             }
             const coords = view.coords;
@@ -21,7 +21,7 @@ export function createViewHighlighter(container) {
                 div.style.width = coords.width + "px";
                 div.style.height = coords.height + "px";
                 div.style.border = "1px solid green";
-                div.style.backgroundColor = "rgba(0, 255, 0, 0.1)";
+                div.style.backgroundColor = "rgba(0, 255, 0, 0.05)";
                 div.style.pointerEvents = "none";
                 container.appendChild(div);
             }